@Test
public void testNnclean() throws Exception {
double[] y = HET_DEL_5X_5N;
double[] nonnoise =
new double[] {260.0736, 197.4272, 194.8618, 1217.8588, 1228.2190, 1151.7017};
double[] result = scorer.nnclean(y, scorer.cleanYIndices(y, 30, 2, 5));
Arrays.sort(result);
Arrays.sort(nonnoise);
assertArrayEquals(nonnoise, result, 0.000001);
}
@Test
public void testLikelihoodSingleComponent() throws Exception {
double[] y = NODEL_ISIZES;
double l = scorer.likelihood(y, new double[] {Math.log(1)}, new double[] {100}, 15);
assertEquals(-29.2070, l, 0.0001);
}
public void testEstimateWNoValues() throws Exception {
double[] y = new double[] {};
double sigma = 30;
double[] initialW = new double[] {Math.log(.5), Math.log(.5)};
assertEquals(1, scorer.estimate(y, initialW, 200, sigma, new double[y.length]).w0, 0.0001);
}
@Test
public void testEstimateW() throws Exception {
double[] y = HET_DEL_5X_5N;
double sigma = 30;
double[] initialW = new double[] {Math.log(.5), Math.log(.5)};
assertEquals(.5, scorer.estimate(y, initialW, 200, sigma, new double[y.length]).w0, 0.0001);
}
@Test
public void testLikelihood() throws Exception {
double[] y = NODEL_ISIZES;
double l =
scorer.likelihood(
y, new double[] {Math.log(.5), Math.log(.5)}, new double[] {100, 1100}, 15);
assertEquals(-29.90017, l, 0.0001);
}
@Test
public void testReduce_homdel_100() throws Exception {
double[] y = NODEL_ISIZES;
ReadGroupInfo readGroupInfo = new ReadGroupInfo();
readGroupInfo.isize = 100;
readGroupInfo.isizeSD = 15;
List<ReadPairInfo> rpis = new ArrayList<ReadPairInfo>();
for (int i = 0; i < y.length; i++) {
double isize = y[i];
ReadPairInfo rpi = new ReadPairInfo();
rpi.insertSize = (int) isize;
rpi.readGroupId = 0;
rpis.add(rpi);
}
Map<Short, ReadGroupInfo> rgis = new HashMap<Short, ReadGroupInfo>();
rgis.put((short) 0, readGroupInfo);
GMMScorerResults results =
scorer.reduceReadPairInfos(rpis.iterator(), rgis, new GenomicLocationWithQuality());
assertEquals(0, results.w0, 0.0001);
}
@Test
public void testNncleanNotEnoughValues() throws Exception {
double[] y = new double[] {260.0736, 1217.8588};
double[] nonnoise = new double[] {};
assertArrayEquals(nonnoise, scorer.nnclean(y, scorer.cleanYIndices(y, 30, 2, 5)), 0.000001);
}
@Test
public void testLogsumexp() throws Exception {
double[] x = new double[] {-7.018195, -309.17497};
assertEquals(-7.018195, scorer.logsumexp(x), 0.00001);
}
@Test
public void testReduce_2_16168700() throws Exception {
double[] y =
new double[] {
492, 549, 558, 517, 562, 523, 533, 537, 544, 546, 540, 506, 516, 519, 560, 515, 498, 546,
493, 518, 520, 517, 153, 164, 189, 208, 154, 203, 540, 194, 497, 566, 551, 555, 139, 491,
510, 229, 199, 190, 213, 190, 151, 210, 218, 226, 186, 173, 171, 226, 212, 181, 216, 146,
171, 184, 214, 199, 192, 184, 136, 208, 214, 226, 203, 200, 217, 176, 174, 222, 182, 186,
188, 202, 211, 190, 216, 163, 201, 244, 241, 216, 254, 189, 189, 158, 213, 240, 203, 238,
241, 178, 195, 196, 213, 225, 187, 239, 219, 171, 235, 227, 216, 163, 214, 220, 195, 180,
189, 206, 211, 178, 206, 207, 201, 205, 203, 197, 221, 215, 215, 161, 199, 136, 203, 212,
172, 211, 222, 180, 157, 207, 187, 202, 188, 191, 180, 197, 197, 199, 209, 237, 255, 174,
187, 212, 215, 218, 142, 201, 150, 155, 206, 192, 182, 156, 201, 248, 195, 206, 165, 178,
217, 184, 178, 164, 167, 130, 196, 195, 139, 211, 191, 176, 212, 195, 149, 226, 199, 247,
168, 223, 176, 198, 196, 226, 144, 196, 213, 191, 203, 173, 188, 186, 265, 222, 219, 209,
218, 206, 226, 208, 188, 240, 172, 210, 198, 155, 206, 163, 183, 165, 197, 168, 135, 225,
226, 190, 222, 189, 152, 245, 212, 231, 193, 150, 162, 210, 185, 217, 244, 233, 167, 100,
169, 187, 203, 141, 189, 214, 158, 154, 164, 210, 220, 176, 208, 184, 218, 157, 171, 184,
203, 200, 189, 187, 223, 199, 174, 194, 210, 155, 145, 189, 250, 209, 174, 196, 165, 262,
219, 182, 196, 206, 201, 180, 168, 212, 187, 215, 207, 243, 170, 195, 210, 146, 244, 271,
134, 147, 220, 206, 206, 214, 167, 192, 173, 181, 185, 234, 189, 207, 218, 185, 221, 165,
244, 247, 251, 195, 170, 204, 183, 183, 201, 202, 169, 183, 243, 186, 202, 207, 195, 134,
146, 165, 214, 217, 180, 187, 166, 219, 179, 204, 190, 172, 204, 159, 247, 217, 234, 215,
196, 216, 178, 235, 190, 225, 181, 228, 243, 201, 215, 239, 231, 232, 215, 150, 224, 189,
212, 192, 208, 237, 189, 155, 279, 182, 214, 200, 176, 211, 236, 231, 208, 177, 235, 207,
221, 189, 222, 209, 241, 191, 226, 232, 217, 179, 208, 193, 217, 164, 218, 192, 186, 147,
190, 255, 203, 187, 197, 159, 179, 217, 214, 191, 187, 210, 194, 205, 161, 188, 147, 204,
165, 170, 191, 170, 254, 170, 187, 149, 206, 209, 180, 172, 277, 219, 245, 198, 206, 181,
115, 235, 188, 146, 219, 251, 176, 196, 221, 252, 238, 217, 164, 220, 213, 183, 200, 169,
140, 182, 201, 259, 175, 179, 245, 173, 208, 184, 171, 210, 161, 185, 197, 225, 229, 162,
228, 239, 151, 176, 175, 191, 185, 172, 210, 222, 196, 244, 155, 210, 226, 206, 202, 226,
182, 203, 211, 54, 183, 162, 218, 178, 222, 186, 175, 185, 206
};
double[] q =
new double[] {
-2.1696611175533603E-10,
-6.785146088283706E-8,
-8.024704012413976E-8,
-1.7379881135464118E-4,
-0.6931471805599502,
-0.693147180559951,
-0.6931471805678728,
-0.693147180572517,
-0.6931471805725841,
-0.6931471805798182,
-0.6931471805997381,
-0.693147180622788,
-0.6931471806495079,
-0.6931471807594544,
-0.6931471845248532,
-0.6931475377340768,
-0.6931503533452836,
-0.6931512316685288,
-0.6931840359492512,
-0.693305956786865,
-0.6937753785184062,
-5.64897333105462,
-7.084857412316782,
-7.354808352597096,
-7.359377330663584,
-7.872364521913692,
-8.04267742026059,
-8.669566545094245,
-8.969160504596012,
-9.221512806273967,
-9.443121607473534,
-9.662320273839363,
-9.89927891367327,
-9.899475907902985,
-10.088747376089458,
-10.136296317056333,
-10.390994468392968,
-10.466896786383858,
-10.54685718548888,
-10.563884362458577,
-10.581221493505096,
-10.62770119673156,
-10.63334549133029,
-10.646393514132974,
-10.657253069096956,
-10.663702915211145,
-10.676735018643225,
-10.681529869083171,
-10.686913818512526,
-10.699011191869902,
-10.712076390390033,
-10.71494371186775,
-10.7264211634449,
-10.740214964542467,
-10.749791882491355,
-10.750311639419573,
-10.754497756231224,
-10.756823839754684,
-10.761609867517738,
-10.766403150113543,
-10.771343223309085,
-10.775062291368782,
-10.77835101998959,
-10.78197573924654,
-10.790276905621603,
-10.795256866828304,
-10.80181701129367,
-10.803087896128151,
-10.80314009117173,
-10.80380175386974,
-10.814394966508459,
-10.81537122505761,
-10.817492173087448,
-10.827675844546354,
-10.829443481011559,
-10.830179309986828,
-10.838212544645792,
-10.844131294622137,
-10.848542068923848,
-10.853854857544324,
-10.856020915168198,
-10.859558263487916,
-10.860158700196953,
-10.880641680567678,
-10.888588199397667,
-10.88874066031219,
-10.91229133295613,
-10.924107483771525,
-10.928346113518579,
-10.92964687162989,
-10.932350396150245,
-10.947241656379116,
-10.960930793781891,
-10.968987987336805,
-10.97537609031065,
-10.97888333176698,
-10.983714693620161,
-10.98396459725721,
-10.988026161635448,
-11.000349775425226,
-11.005190098864151,
-11.008058181344321,
-11.019278024115216,
-11.021291910823129,
-11.028322692242273,
-11.029149326715867,
-11.061707802901795,
-11.068395939657464,
-11.069852995949653,
-11.069933889625611,
-11.076805056632331,
-11.083382084815497,
-11.08509571105233,
-11.089824851323177,
-11.089885487887706,
-11.094113103444364,
-11.100555423526552,
-11.10133122503366,
-11.113614986629823,
-11.120602422354539,
-11.145674693493445,
-11.155171514432995,
-11.155584476787158,
-11.16235322235817,
-11.1743979194754,
-11.179930631664496,
-11.18119861073529,
-11.186147109040785,
-11.186253203506407,
-11.194110915846878,
-11.199850352222427,
-11.205512744495765,
-11.206608319859358,
-11.208810637615429,
-11.208935886080297,
-11.212548365317536,
-11.21424709756695,
-11.23214588034072,
-11.23570216013649,
-11.241624346768159,
-11.244808957153834,
-11.266084963986366,
-11.268474719034423,
-11.274459210338485,
-11.277656936264519,
-11.287998772134518,
-11.29176173512852,
-11.32731360798145,
-11.3311640427555,
-11.333039066255113,
-11.337135957453896,
-11.358383144232379,
-11.366000617155429,
-11.36659303658937,
-11.384491692834233,
-11.393971852444107,
-11.397996304813965,
-11.398666888576694,
-11.402682214394648,
-11.405528284621504,
-11.407568257147572,
-11.407675455579561,
-11.41065714680622,
-11.413605020736467,
-11.4148346590077,
-11.415836742763219,
-11.420320556150081,
-11.428985678366118,
-11.433031937419411,
-11.434169066321804,
-11.435919487005071,
-11.440941652690302,
-11.448930587418992,
-11.452612464056163,
-11.453244486778988,
-11.456067248558421,
-11.459937035668403,
-11.465816007733807,
-11.4667715838359,
-11.469548419058178,
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-11.571770761162302,
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-11.607173819094001,
-11.607813409351401,
-11.609557604640045,
-11.612361592929172,
-11.616746254410995,
-11.617624768597299,
-11.619735777410394,
-11.627618299073958,
-11.62944394218113,
-11.632677032446942,
-11.633634976353044,
-11.656295440568524,
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-11.684179635522574,
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-11.69307353975453,
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-11.718261062653541,
-11.721859752278295,
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-11.907464313404134,
-11.919426054164733,
-11.936547937965024,
-11.948251494311359,
-11.960643538424119,
-11.964765517009852,
-11.971871206040912,
-11.979188840635903,
-11.979872541286628,
-11.980059958768567,
-11.983324560267182,
-11.989347998124508,
-11.990776747102908,
-11.99889265952341,
-12.008243796387097,
-12.023278749706506,
-12.031611349208564,
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-12.049962180295484,
-12.051187384115412,
-12.05373847617144,
-12.059378026508043,
-12.061165014529005,
-12.08425921677133,
-12.09290153858423,
-12.096657564011192,
-12.104708475256558,
-12.105411877986661,
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-12.125078259994385,
-12.128819793798097,
-12.131577706216952,
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-12.176385324600925,
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-12.217147145466207,
-12.223044019810153,
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-12.240297236766862,
-12.246202784275956,
-12.247633359841192,
-12.249949482076318,
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-12.259958059662193,
-12.269491325434306,
-12.271041060855865,
-12.271560124839013,
-12.278694185360683,
-12.27872132138998,
-12.281563915928338,
-12.28822897720492,
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-12.308269982919533,
-12.327691266877867,
-12.336869339082376,
-12.341056064100963,
-12.356900031894881,
-12.376800778971106,
-12.380930491424309,
-12.399361188991575,
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-12.400505214268058,
-12.415877378043504,
-12.418190646488394,
-12.428500964237001,
-12.434414081290308,
-12.454876625161518,
-12.456919070770772,
-12.469664441900012,
-12.493521693362812,
-12.494697985905036,
-12.504294353427472,
-12.520024626960016,
-12.535297564869646,
-12.539342819183414,
-12.540348346241775,
-12.554023456234265,
-12.559622674013278,
-12.571204825571195,
-12.574741730551908,
-12.583825658741782,
-12.626304184802747,
-12.627749295535345,
-12.637190715097805,
-12.647945005733536,
-12.669042955168685,
-12.675206250932629,
-12.681832925909207,
-12.687801255687505,
-12.691598881155024,
-12.711106689629208,
-12.73904118528932,
-12.742302306626886,
-12.74955717594839,
-12.765080380251657,
-12.768093773024798,
-12.775903088506945,
-12.823522421893,
-12.826894576679015,
-12.827617882552838,
-12.831061272166139,
-12.831646753233883,
-12.843083873122257,
-12.86085924799955,
-12.903402521217178,
-12.906104025278378,
-12.906447168159744,
-12.910875138821364,
-12.91455067260042,
-12.934919274290205,
-12.956163559665734,
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-12.97051594259994,
-12.9753163463167,
-12.984005448337019,
-12.999829630789407,
-13.045536310822637,
-13.048772683530792,
-13.052781597159033,
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-13.093911862249723,
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-13.152551785535437,
-13.154477154375927,
-13.161777998003828,
-13.167025161781197,
-13.169691464089375,
-13.181291817433694,
-13.182216311875594,
-13.219039826262367,
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-13.227825837956352,
-13.232727488905265,
-13.252450113577616,
-13.25439216258476,
-13.264044774348491,
-13.287510294333067,
-13.297580706956184,
-13.323571082504627,
-13.334592054896639,
-13.360688679044983,
-13.376950374813497,
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-13.400183248891341,
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-13.451586983108424,
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-13.629226177962948,
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-13.954565735702303,
-13.962626346683482,
-14.011017965921496,
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-14.264723939869263,
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-14.435348487784918,
-14.443018727672229,
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-18.45900866840194,
-18.607842667340645,
-19.147320224015054,
-19.35446227099996,
-19.538798616221108,
-19.600596948545835
};
ReadGroupInfo readGroupInfo = new ReadGroupInfo();
readGroupInfo.isize = 200;
readGroupInfo.isizeSD = 30;
List<ReadPairInfo> rpis = new ArrayList<ReadPairInfo>();
for (int i = 0; i < y.length; i++) {
double isize = y[i];
ReadPairInfo rpi = new ReadPairInfo();
rpi.insertSize = (int) isize;
rpi.readGroupId = 0;
rpi.pMappingCorrect = q[i];
rpis.add(rpi);
}
scorer.setMaxLogMapqDiff(5);
scorer.setMinCoverage(3);
Map<Short, ReadGroupInfo> rgis = new HashMap<Short, ReadGroupInfo>();
rgis.put((short) 0, readGroupInfo);
GMMScorerResults results =
scorer.reduceReadPairInfos(rpis.iterator(), rgis, new GenomicLocationWithQuality());
assertEquals(0, results.w0, 0.0001);
}